Variant report

Variant	rs542175
Chromosome Location	chr11:64806270-64806271
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF384	chr11:64806098-64806725	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:64806238-64806274	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64788946..64793194-chr11:64803720..64806785,4	K562	blood:
2	chr11:64799194..64801472-chr11:64804094..64806308,2	MCF-7	breast:
3	chr11:64798286..64800870-chr11:64805869..64808336,2	K562	blood:
4	chr11:64645854..64647856-chr11:64806233..64808621,2	K562	blood:
5	chr11:64804612..64806945-chr11:64807096..64809851,2	MCF-7	breast:
6	chr11:64805658..64811611-chr11:64862545..64865451,9	MCF-7	breast:
7	chr11:64804480..64810811-chr11:64850224..64856247,12	K562	blood:

No data

Variant related genes	Relation type
SAC3D1	TF binding region
ENSG00000168061	Chromatin interaction
ENSG00000110047	Chromatin interaction
ENSG00000213465	Chromatin interaction
ENSG00000146670	Chromatin interaction
ENSG00000162300	Chromatin interaction
ENSG00000149823	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10088	0.82[CEU][hapmap];0.94[GIH][hapmap]
rs10160811	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10792455	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1195975	0.94[GIH][hapmap]
rs1195978	0.94[GIH][hapmap]
rs1196047	0.94[GIH][hapmap]
rs1196051	0.82[CEU][hapmap]
rs1209621	0.94[GIH][hapmap]
rs1211975	0.94[GIH][hapmap]
rs1300836	0.94[GIH][hapmap]
rs17146589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2458589	0.81[ASN][1000 genomes]
rs2670910	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34589041	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3896078	0.94[GIH][hapmap]
rs473587	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs481446	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs484147	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs494837	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs495820	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs495935	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs497023	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs500464	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs508375	0.94[GIH][hapmap]
rs527039	0.94[GIH][hapmap]
rs533164	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs533301	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs550771	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs561524	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs584698	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs608772	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs613352	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs633671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs664118	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689361	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7939766	0.82[CEU][hapmap]
rs907629	0.90[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	nsv897709	chr11:64772545-64870779	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv897710	chr11:64772545-64885445	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
4	nsv897711	chr11:64772545-64900270	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64795200-64808000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:64795400-64808000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:64795600-64808000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr11:64795800-64807800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr11:64795800-64807800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr11:64795800-64808000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr11:64795800-64808000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr11:64796000-64807400	Weak transcription	Stomach Mucosa	stomach
9	chr11:64796000-64807600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr11:64796000-64807800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr11:64796000-64807800	Weak transcription	Fetal Kidney	kidney
12	chr11:64796000-64808000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr11:64796200-64807200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr11:64796200-64807200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr11:64796200-64807200	Weak transcription	K562	blood
16	chr11:64796200-64807800	Weak transcription	Small Intestine	intestine
17	chr11:64796200-64807800	Weak transcription	A549	lung
18	chr11:64796200-64807800	Weak transcription	HMEC	breast
19	chr11:64796200-64807800	Weak transcription	HUVEC	blood vessel
20	chr11:64796200-64807800	Weak transcription	NHEK	skin
21	chr11:64796200-64808000	Weak transcription	Osteobl	bone
22	chr11:64796400-64807400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr11:64796400-64807400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr11:64796400-64807600	Weak transcription	Fetal Brain Male	brain
25	chr11:64796400-64807800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr11:64796600-64807600	Strong transcription	Fetal Intestine Small	intestine
27	chr11:64796800-64807400	Strong transcription	Fetal Muscle Leg	muscle
28	chr11:64796800-64808000	Strong transcription	Fetal Stomach	stomach
29	chr11:64798200-64806400	Strong transcription	Placenta	Placenta
30	chr11:64798400-64807400	Strong transcription	Skeletal Muscle Male	skeletal muscle
31	chr11:64798400-64807800	Strong transcription	Fetal Intestine Large	intestine
32	chr11:64798400-64807800	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr11:64798600-64807200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr11:64798600-64807600	Strong transcription	Brain Germinal Matrix	brain
35	chr11:64798600-64807600	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr11:64798600-64807800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr11:64798800-64806400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr11:64798800-64806400	Strong transcription	Fetal Thymus	thymus
39	chr11:64798800-64806600	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr11:64798800-64807000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr11:64798800-64807400	Strong transcription	Adipose Nuclei	Adipose
42	chr11:64798800-64807600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr11:64798800-64807600	Strong transcription	Rectal Smooth Muscle	rectum
44	chr11:64799000-64806400	Strong transcription	Ovary	ovary
45	chr11:64799000-64806400	Strong transcription	Spleen	Spleen
46	chr11:64799000-64807600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr11:64799000-64807600	Strong transcription	Right Ventricle	heart
48	chr11:64799200-64806400	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr11:64799400-64806400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr11:64799400-64806400	Strong transcription	Thymus	Thymus

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